P. Bushel

发表

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

David P. Kreil, Todd M. Smith, Thomas M. Blomquist, 2014, Nature Biotechnology.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Kevin C. Dorff, Aaron M. Smalter, Stephen C. Harris, 2010, Nature Biotechnology.

Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals.

Daniel Krewski, Russell S Thomas, Carole L Yauk, 2015, Regulatory toxicology and pharmacology : RTP.

Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes

P. Bushel, J. Chou, 2009, BMC Genomics.

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

John Quackenbush, J. Corton, S. Hester, 2008, BMC Genomics.

Revealing a human p53 universe

Brian D. Bennett, Christopher A. Lavender, Sara A. Grimm, 2018, Nucleic acids research.

p53 integrates host defense and cell fate during bacterial pneumonia

P. Bushel, Leping Li, M. A. Resnick, 2013, The Journal of experimental medicine.

Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals.

P. Bushel, R. Paules, J. Chou, 2013, Physiological genomics.

Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

P. Bushel, R. Paules, J. Chou, 2007, Molecular Cancer Research.

Profiles of Global Gene Expression in Ionizing-Radiation–Damaged Human Diploid Fibroblasts Reveal Synchronization behind the G1 Checkpoint in a G0-like State of Quiescence

Pierre R. Bushel, Thomas E. Mullen, Richard S. Paules, 2005, Environmental health perspectives.

Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells.

Lee Bennett, Pierre R Bushel, Cynthia A Afshari, 2003, Molecular cancer research : MCR.

Blood gene expression signatures predict exposure levels

R. E. Wilson, R. Tennant, P. Bushel, 2007, Proceedings of the National Academy of Sciences.

Editorial: Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences

Pierre R. Bushel, P. Bushel, Weida Tong, 2018, Front. Genet..

Platforms for biomarker analysis using high-throughput approaches in genomics, transcriptomics, proteomics, metabolomics, and bioinformatics.

B Alex Merrick, Pierre R Bushel, Richard S Paules, 2011, IARC scientific publications.

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

David P. Kreil, Paweł P. Łabaj, C. Furlanello, 2014, Nature Biotechnology.

A comprehensive study design reveals treatment-and transcript abundance – dependent concordance between RNA-seq and microarray data

David P. Kreil, Paweł P. Łabaj, Dalila, 2014 .

Consistency of predictive signature genes and classifiers generated using different microarray platforms

Tieliu Shi, T. Nikolskaya, Y. Nikolsky, 2010, The Pharmacogenomics Journal.

Standardizing global gene expression analysis between laboratories and across platforms

Kathleen F. Kerr, Roger E Bumgarner, H. Dressman, 2005, Nature Methods.

The evolution of bioinformatics in toxicology: advancing toxicogenomics.

P. Bushel, C. Afshari, H. Hamadeh, 2011, Toxicological sciences : an official journal of the Society of Toxicology.

Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling.

P. Bushel, Jun Lu, 2013, Gene.

Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays

P. Bushel, S. Peddada, Jun Lu, 2011, Nucleic acids research.

Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health.

Molly A. Hall, D. Wishart, P. Bushel, 2017, Annual review of public health.

EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data

P. Bushel, Jianying Li, 2016, BMC Genomics.

Sources of variance in baseline gene expression in the rodent liver.

Raegan B O'Lone, J. Corton, P. Bushel, 2012, Mutation research.

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers

Raegan B O'Lone, P. Bushel, Jianying Li, 2020, RNA biology.

Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype

B Alex Merrick, Pierre R Bushel, Richard S Paules, 2008, Genome Biology.

Genomic indicators in the blood predict drug-induced liver injury

H Fang, T. Nikolskaya, Y. Nikolsky, 2010, The Pharmacogenomics Journal.

Regulation of DNA Replication Fork Genes by 17β-Estradiol

E. Lobenhofer, P. Bushel, Leping Li, 2002 .

Regulation of DNA replication fork genes by 17beta-estradiol.

E. Lobenhofer, P. Bushel, Leping Li, 2002, Molecular endocrinology.

Gene expression analysis reveals chemical-specific profiles.

Lee Bennett, Kerry Blanchard, Supriya Jayadev, 2002, Toxicological sciences : an official journal of the Society of Toxicology.

The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling.

Ruchir R Shah, Pierre R Bushel, Nisha S Sipes, 2019, Toxicological sciences : an official journal of the Society of Toxicology.

Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base.

R. Tennant, M. Waters, S. Stasiewicz, 2002 .

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.

N. Morrison, M. Waters, K. Tomer, 2005, Toxicological sciences : an official journal of the Society of Toxicology.

Methapyrilene Toxicity: Anchorage of Pathologic Observations to Gene Expression Alterations

Kerry Blanchard, Supriya Jayadev, Pierre R Bushel, 2002, Toxicologic pathology.

Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data

S. Auerbach, P. Bushel, R. Paules, 2020, Frontiers in Genetics.

Toxicogenomics: Gene Expression Analysis and Computational Tools

J. Corton, J. Auman, P. Bushel, 2006 .

A short, highly repetitive element in intron -1 of the human c-Ha-ras gene acts as a block to transcriptional readthrough by a viral promoter

P. Bushel, J. Wu, L. Mendelsohn, 1990 .

A Collaborative Initiative to Establish Genomic Biomarkers for Assessing Tumorigenic Potential to Reduce Reliance on Conventional Rodent Carcinogenicity Studies

Kamin J. Johnson, A. Podtelezhnikov, J. Corton, 2022, Toxicological sciences : an official journal of the Society of Toxicology.

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database

Raegan B O'Lone, P. Bushel, Jianying Li, 2018, BMC Genomics.

Population Differences in Transcript-Regulator Expression Quantitative Trait Loci

Xihong Lin, Winston A Hide, P. Bushel, 2012, PloS one.

Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity

P. Bushel, Jianying Li, Myrtle A. Davis, 2015, Front. Genet..

Regulation of smooth muscle alpha-actin promoter in ras-transformed cells: usefulness for setting up reporter gene-based assay system for drug screening.

P. Bushel, C. Kumar, F. Ramirez, 1992, Cancer research.

Effects of mannose-binding lectin on pulmonary gene expression and innate immune inflammatory response to ozone.

P. Bushel, Jianying Li, S. Kleeberger, 2016, American journal of physiology. Lung cellular and molecular physiology.

Blood gene expression profiling of an early acetaminophen response

P. Bushel, P. Watkins, R. Paules, 2016, The Pharmacogenomics Journal.

Two proximal CArG elements regulate SM alpha-actin promoter, a genetic marker of activated phenotype of mesangial cells.

P. Bushel, W. Herman, C. Kumar, 1995, The American journal of physiology.

Blood transcript immune signatures distinguish a subset of people with elevated serum ALT from others given acetaminophen

P. Bushel, P. Watkins, R. Paules, 2016, Clinical pharmacology and therapeutics.

The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages

P. Bushel, R. Mason, D. Ganini da Silva, 2018, Inflammation Research.

Prediction of compound signature using high density gene expression profiling.

Lee Bennett, Kerry Blanchard, Supriya Jayadev, 2002, Toxicological sciences : an official journal of the Society of Toxicology.

Novel Roles for Notch3 and Notch4 Receptors in Gene Expression and Susceptibility to Ozone-Induced Lung Inflammation in Mice

P. Bushel, S. Kleeberger, W. Gladwell, 2015, Environmental health perspectives.

Elucidation of Mechanisms of Topotecan-Induced Cell Death in Human Breast MCF-7 Cancer Cells by Gene Expression Analysis

P. Bushel, E. Tokar, B. Sinha, 2020, Frontiers in Genetics.

Smooth Muscle α-Actin Promoter Activity Is Induced by Serum Stimulation of Fibroblast Cells

P. Bushel, C. Kumar, Jae-Hong Kim, 1993 .

Smooth muscle alpha-actin promoter activity is induced by serum stimulation of fibroblast cells.

P. Bushel, C. Kumar, J. Kim, 1993, Biochemical and biophysical research communications.

Identification of Identical Transcript Changes in Liver and Whole Blood during Acetaminophen Toxicity

P. Bushel, P. Watkins, J. Chou, 2012, Front. Gene..

A short, highly repetitive element in intron -1 of the human c-Ha-ras gene acts as a block to transcriptional readthrough by a viral promoter

P. Bushel, J. Wu, N. Lowndes, 1990, Molecular and cellular biology.

Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element

P. Bushel, G. Grindlay, J. Wu, 1990, Molecular and cellular biology.

Short‐term tetrabromobisphenol A exposure promotes fibrosis of human uterine fibroid cells in a 3D culture system through TGF‐beta signaling

P. Bushel, D. Dixon, Erica Scappini, 2022, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development

P. Bushel, L. Mendelsohn, M. Allan, 1990, Molecular and cellular biology.

Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity

Brian D. Bennett, P. Bushel, B. Bennett, 2019, The Journal of Biological Chemistry.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Paul M. Rindler, Ira W. Deveson, S. Cawley, 2021, Nature Biotechnology.

Global Gene Profiling of Spontaneous Hepatocellular Carcinoma in B6C3F1 Mice

S. Auerbach, P. Bushel, S. Peddada, 2011, Toxicologic pathology.

Identification of Primary Transcriptional Regulation of Cell Cycle-Regulated Genes upon DNA Damage

P. Hurban, R. Elkon, E. Lobenhofer, 2007, Cell cycle.

The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog

P. Bushel, Jianying Li, M. Farmen, 2016, BMC Genomics.

Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models

Pierre R. Bushel, Russell D. Wolfinger, Greg Gibson, 2001, J. Comput. Biol..

DNA methylation in mice is influenced by genetics as well as sex and life experience

Brian D. Bennett, Sara A. Grimm, J. Mullikin, 2019, Nature Communications.

Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells

Sara A. Grimm, P. Bushel, F. Tyson, 2018, G3: Genes, Genomes, Genetics.

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database

P. Bushel, Jianying Li, J. Calley, 2018, BMC Genomics.

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver

Brian D. Bennett, Sara A. Grimm, G. Bouffard, 2018, Scientific Reports.

p53 and NF-κB coregulate proinflammatory gene responses in human macrophages.

P. Bushel, D. Menendez, M. Shatz, 2014, Cancer research.

LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells

Brian D. Bennett, Sara A. Grimm, S. Luo, 2015, Molecular and Cellular Biology.

Global Transcriptome and Deletome Profiles of Yeast Exposed to Transition Metals

Pierre R. Bushel, P. Bushel, J. Freedman, 2008, PLoS genetics.

Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae.

T. Kunkel, P. Bushel, R. Kerns, 2012, DNA repair.

A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples

Pierre R. Bushel, Scott S. Auerbach, Richard S. Paules, 2018, Front. Genet..

Development of gut microbiota in infants not exposed to medical interventions

D. Baird, P. Bushel, S. Peddada, 2011, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

Differential toxicogenomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in malignant and nonmalignant human airway epithelial cells.

P. Bushel, C. Afshari, Takashi Takahashi, 2002, Toxicological sciences : an official journal of the Society of Toxicology.

Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation

P. Bushel, Jianying Li, N. Chandel, 2018, PLoS biology.

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

Tieliu Shi, Leming Shi, W. Tong, 2010, The Pharmacogenomics Journal.

CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data

Pierre R. Bushel, Hui Gong, Asif Rashid, 2007, Nucleic Acids Res..

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

David P. Kreil, Paweł P. Łabaj, Jeff S. Jasper, 2021, Genome biology.

Human Macrophages B Coregulate Proinflammatory Gene Responses in κ p 53 and NF-Updated

P. Bushel, D. Menendez, M. Shatz, 2014 .

Microenvironment and Immunology p 53 and NFk B Coregulate Proin fl ammatory Gene Responses in Human Macrophages

P. Bushel, D. Menendez, M. Shatz, 2014 .

Responses in Human Macrophages

P. Bushel, D. Menendez, M. Shatz, 2014 .

Research resource: whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq.

Sara A. Grimm, P. Bushel, Leping Li, 2012, Molecular endocrinology.

Insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells.

P. Bushel, J. Oh, C. Afshari, 2002, Neoplasia.

Insulin-Like Growth Factor-1 Inscribes a Gene Expression Profile for Angiogenic Factors and Cancer Progression in Breast Epithelial Cells 1

P. Bushel, J. Oh, C. Afshari, 2002 .

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Paul M. Rindler, David P. Kreil, Paweł P. Łabaj, 2021, Genome biology.

STATISTICAL ANALYSIS OF A GENE EXPRESSION MICROARRAY EXPERIMENT WITH REPLICATION

Pierre R. Bushel, Gary A. Churchill, M. Kathleen Kerr, 2002 .

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

Pierre R. Bushel, Nicholas A. Heard, Liwen Liu, 2009, BMC Systems Biology.

Inactivation of DNA Mismatch Repair by Increased Expression of Yeast MLH1

Pierre R. Bushel, Cynthia A. Afshari, Thomas A. Kunkel, 2001, Molecular and Cellular Biology.

Maximizing biomarker discovery by minimizing gene signatures

Weida Tong, Jennifer Fostel, Youping Deng, 2011, BMC Genomics.

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes

Pierre R. Bushel, David M. Reif, Stephen W. Edwards, 2013, BMC Systems Biology.

Progress in the application of DNA microarrays.

E. Lobenhofer, P. Bushel, C. Afshari, 2001, Environmental health perspectives.

Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased

Pierre R. Bushel, Richard S. Paules, Jeff W. Chou, 2005, J. Bioinform. Comput. Biol..

Differential Transcriptomic Analysis of Spontaneous Lung Tumors in B6C3F1 Mice: Comparison to Human Non–Small Cell Lung Cancer

S. Auerbach, P. Bushel, S. Peddada, 2012, Toxicologic pathology.

ATM Requirement in Gene Expression Responses to Ionizing Radiation in Human Lymphoblasts and Fibroblasts

P. Bushel, R. Paules, W. Kaufmann, 2006, Molecular Cancer Research.

Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism

P. Bushel, Adam S. Mastrocola, R. Tibbetts, 2016, Nucleic acids research.

Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription

P. Bushel, Ahsan Huda, 2013, Transcriptomics: open access.

Structural Equation Modeling of In silico Perturbations

P. Bushel, Jianying Li, F. DeMayo, 2021, Frontiers in Genetics.

Computational selection of distinct class- and subclass-specific gene expression signatures

Pierre R. Bushel, James Green, Lee Bennett, 2002, J. Biomed. Informatics.

Alterations in apoptotic signaling in human idiopathic cardiomyopathic hearts in failure.

P. Bushel, A. Haugen, C. Afshari, 2003, American journal of physiology. Heart and circulatory physiology.

Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation

P. Bushel, Leping Li, R. Paules, 2003, Molecular carcinogenesis.

Principal Variance Components Analysis: Estimating Batch Effects in Microarray Gene Expression Data

T. Chu, R. Wolfinger, P. Bushel, 2009 .

Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53

S. Auerbach, P. Bushel, K. Funderburk, 2017, Front. Genet..

Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification

Pierre R. Bushel, Hao Helen Zhang, Zhao-Bang Zeng, 2013, Cancer informatics.

Clustering of Gene Expression Data and End-Point Measurements by Simulated Annealing

Pierre R. Bushel, P. Bushel, 2009, J. Bioinform. Comput. Biol..

Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes

Pierre R. Bushel, Russell D. Wolfinger, Greg Gibson, 2007, BMC Systems Biology.

Secondhand Smoke‐Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture‐Induced Specific Mitogenic and Pro‐inflammatory Cell Signaling Events in Lung Epithelial Cells

P. Bushel, A. Bauer, B. Upham, 2017, Toxicological sciences : an official journal of the Society of Toxicology.

MAPS: a microarray project system for gene expression experiment information and data validation

Kate Johnson, Pierre R. Bushel, Lee Bennett, 2001, Bioinform..

ATM-Dependent and -Independent Gene Expression Changes in Response to Oxidative Stress, Gamma Irradiation, and UV Irradiation

P. Bushel, Leping Li, R. Paules, 2003, Radiation research.

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

Tong Zhou, Pierre R. Bushel, Richard S. Paules, 2007, BMC Bioinformatics.

Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes

Brian D. Bennett, E. Perez-stable, Jung S. Byun, 2020, Science Advances.

Discovery in toxicology: Mediation by gene expression array technology

P. Bushel, R. Paules, C. Afshari, 2001, Journal of biochemical and molecular toxicology.

Database development in toxicogenomics: issues and efforts.

Michael D Waters, Susanna-Assunta Sansone, Pierre R Bushel, 2004, Environmental health perspectives.

Supplementary Tables 1–6

Tieliu Shi, T. Nikolskaya, Y. Nikolsky, 2010 .

Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology

P. Bushel, Jianying Li, James M. Ward, 2022, Scientific Reports.

A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics

Brian E. Howard, Richard S Judson, Brian E Howard, 2018, PloS one.

Gene Expression in Uterine Leiomyoma from Tumors Likely to Be Growing (from Black Women over 35) and Tumors Likely to Be Non-Growing (from White Women over 35)

D. Baird, P. Bushel, S. Peddada, 2013, PloS one.

EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data

P. Bushel, Jianying Li, 2016, BMC Genomics.

Structure and IgE cross-reactivity among walnut and peanut vicilin leader sequences

C. Schein, P. Bushel, S. Maleki, 2021 .

Structure, Immunogenicity, and IgE Cross-Reactivity among Walnut and Peanut Vicilin-Buried Peptides.

C. Schein, P. Bushel, S. Maleki, 2022, Journal of Agricultural and Food Chemistry.

Gene Expression Profiling Elucidates Cellular Responses to NCX4040 in Human Ovarian Tumor Cells: Implications in the Mechanisms of Action of NCX4040

P. Bushel, Jianying Li, E. Tokar, 2022, Cancers.

DNA methylation in mice is influenced by genetics as well as sex and life experience

Brian D. Bennett, Sara A. Grimm, J. Mullikin, 2019, Nature Communications.

Zhao-Bang Zeng, Pierre R Bushel, Richard S Paules, 2008, BMC Genomics.

Development of Phenotypic and Transcriptional Biomarkers to Evaluate Relative Activity of Potentially Estrogenic Chemicals in Ovariectomized Mice

P. Bushel, K. Korach, J. Foley, 2015, Environmental health perspectives.

Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity.

Kerry Blanchard, Supriya Jayadev, Cynthia A Afshari, 2004, Mutation research.

Addendum: Standardizing global gene expression analysis between laboratories and across platforms

Kathleen F. Kerr, Roger E Bumgarner, H. Dressman, 2005, Nature Methods.

Genomic interrogation of mechanism(s) underlying cellular responses to toxicants.

Lee Bennett, Pierre R Bushel, Richard S Paules, 2002, Toxicology.

Two serum response elements mediate transcriptional repression of human smooth muscle alpha-actin promoter in ras-transformed cells.

P. Bushel, H. Ruley, J. Catino, 1995, Oncogene.

Toward a checklist for exchange and interpretation of data from a toxicology study.

Susan Hester, Weida Tong, Stephen W. Edwards, 2007, Toxicological sciences : an official journal of the Society of Toxicology.

PAGE: phase-shifted analysis of gene expression

Elo Leung, Pierre R. Bushel, P. Bushel, 2006, Bioinform..

Gene expression PAGE : phase-shifted analysis of gene expression

P. Bushel, Elo Leung, 2006 .

Gene expression pattern recognition algorithm inferences to classify samples exposed to chemical agents

James R. Green, Lee Bennett, Alan Ableson, 2002, SPIE BiOS.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application

Pierre R. Bushel, Jennifer Fostel, Michael D. Waters, 2006, Bioinform..

Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences

P. Bushel, Weida Tong, 2019, Frontiers Research Topics.

Discovery in toxicology: Mediation by gene expression array technology

P. Bushel, R. Paules, C. Afshari, 2001, Journal of biochemical and molecular toxicology.

Systems Toxicology and the Chemical Effects in Biological Systems (CEBS) Knowledge Base

M Waters, M. Waters, S. Stasiewicz, 2003, EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences.

Detection of diluted gene expression alterations using cDNA microarrays.

P. Bushel, R. Paules, C. J. Tucker, 2002, BioTechniques.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Todd H. Stokes, Kevin C. Dorff, Aaron M. Smalter, 2010, Nature Biotechnology.

Development of gut microbiota in infants not exposed to medical interventions

D. Baird, P. Bushel, S. Peddada, 2011, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

Dissecting the Fission Yeast Regulatory Network Reveals Phase- Specific Control Elements of Its Cell Cycle Dissecting the Fission Yeast Regulatory Network Reveals Phase-specific Control Elements of Its Cell Cycle

P. Bushel, S. Peddada, C. Link, 2022 .

Toxicogenomics: Gene Expression Analysis and Computational Tools

J. Corton, J. Auman, P. Bushel, 2006 .

Transcriptomic profiles of tissues from rats treated with anticancer drug combinations

P. Bushel, Jianying Li, Myrtle A. Davis, 2019, Scientific Data.

goSTAG: gene ontology subtrees to tag and annotate genes within a set

Pierre R. Bushel, Brian D. Bennett, P. Bushel, 2017, Source Code for Biology and Medicine.

Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acid

P. Bushel, B. Chorley, G. Carswell, 2024, Frontiers in oncology.

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

P. Bushel, S. Peddada, N. Heard, 2009, BMC Systems Biology.